It should... My current game is Bobs and Whistlestop and I'm all the way to yellow science in it. If you're playing an earlier version there were a couple recipes that didn't work right, but I've fixed that. Pretty much all Bobs recipes are supported by either the big assembly machine or the big furnace. A couple of the recipes made in special buildings I left alone, if I recall correctly it's the pump that makes oxygen, hydrogen, nitrogen that might need to be still used.
